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pathwayPCA: an R package for integrative pathway analysis with modern PCA methodology and gene selection

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/gepi.20532openalex-snapshot

Pathway‐based analysis for genome‐wide association studies using supervised principal components

inferredcites →https://doi.org/10.1007/s10741-010-9197-zopenalex-snapshot

Hypertension, left ventricular hypertrophy and chronic kidney disease

inferredcites →https://doi.org/10.1016/j.ccell.2016.04.001openalex-snapshot

Comprehensive Characterization of Molecular Differences in Cancer between Male and Female Patients

inferredcites →https://doi.org/10.1016/j.cell.2016.05.069openalex-snapshot

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

inferredcites →https://doi.org/10.1016/j.ygeno.2011.04.006openalex-snapshot

Gene set analysis of genome-wide association studies: Methodological issues and perspectives

inferredcites →https://doi.org/10.1038/nature13438openalex-snapshot

Proteogenomic characterization of human colon and rectal cancer

inferredcites →https://doi.org/10.1038/nmeth.3252openalex-snapshot

Orchestrating high-throughput genomic analysis with Bioconductor

inferredcites →https://doi.org/10.1073/pnas.0506580102openalex-snapshot

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

inferredcites →https://doi.org/10.1093/bioinformatics/btg382openalex-snapshot

A global test for groups of genes: testing association with a clinical outcome

inferredcites →https://doi.org/10.1093/bioinformatics/btl567openalex-snapshot

Using GOstats to test gene lists for GO term association

inferredcites →https://doi.org/10.1093/bioinformatics/btm051openalex-snapshot

Analyzing gene expression data in terms of gene sets: methodological issues

inferredcites →https://doi.org/10.1093/bioinformatics/btn458openalex-snapshot

Supervised principal component analysis for gene set enrichment of microarray data with continuous or survival outcomes

inferredcites →https://doi.org/10.1093/bioinformatics/btu393openalex-snapshot

circlize implements and enhances circular visualization in R

inferredcites →https://doi.org/10.1093/nar/gkv1024openalex-snapshot

WikiPathways: capturing the full diversity of pathway knowledge

inferredcites →https://doi.org/10.1093/nar/gkx1090openalex-snapshot

LinkedOmics: analyzing multi-omics data within and across 32 cancer types

inferredcites →https://doi.org/10.1101/326470openalex-snapshot

The UCSC Xena platform for public and private cancer genomics data visualization and interpretation

inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot

Circos: An information aesthetic for comparative genomics

inferredcites →https://doi.org/10.1161/jaha.117.005838openalex-snapshot

A Systems Biology Approach to Investigating Sex Differences in Cardiac Hypertrophy

inferredcites →https://doi.org/10.1186/gb-2011-12-4-r41openalex-snapshot

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

inferredcites →https://doi.org/10.1214/08-aos625openalex-snapshot

On the adaptive elastic-net with a diverging number of parameters

inferredcites →https://doi.org/10.1253/circj.cj-10-0196openalex-snapshot

Sex and Gender Differences in Myocardial Hypertrophy and Heart Failure

inferredcites →https://doi.org/10.1371/journal.pone.0156895openalex-snapshot

A Comparative Study of Five Association Tests Based on CpG Set for Epigenome-Wide Association Studies

inferredcites →https://doi.org/10.2202/1544-6115.1697openalex-snapshot

Adaptive Elastic-Net Sparse Principal Component Analysis for Pathway Association Testing

inferredcites →https://doi.org/10.3389/fphys.2015.00383openalex-snapshot

Pathway Analysis: State of the Art

inferredcites →https://doi.org/10.5114/wo.2014.47136openalex-snapshot

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.stem.2021.04.006openalex-snapshot

Generation of hypothalamic arcuate organoids from human induced pluripotent stem cells

inferred← citeshttps://doi.org/10.1093/biostatistics/kxaa029openalex-snapshot

Individualized multi-omic pathway deviation scores using multiple factor analysis

inferred← citeshttps://doi.org/10.1186/s13059-020-02139-4openalex-snapshot

COCOA: coordinate covariation analysis of epigenetic heterogeneity

inferred← citeshttps://doi.org/10.3233/jad-210128openalex-snapshot

PRESENILIN 1 Mutations Causing Early-Onset Familial Alzheimer’s Disease or Familial Acne Inversa Differ in Their Effects on Genes Facilitating Energy Metabolism and Signal Transduction

inferred← citeshttps://doi.org/10.3389/fonc.2020.00423openalex-snapshot

Computational Oncology in the Multi-Omics Era: State of the Art

inferred← citeshttps://doi.org/10.3390/metabo9100200openalex-snapshot

The metaRbolomics Toolbox in Bioconductor and beyond

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